1386P - Validation of MET amplification using next-generation sequencing in lung adenocarcinoma

Background

MET gene amplification is a potential therapeutic target in lung adenocarcinoma (LUAD) currently identified by fluorescence in situ hybridization (FISH). Next-generation sequencing (NGS) has become an essential diagnostic tool for routine biomarker profiling of cancer patients, including the detection of copy number alterations (CNAs). The aim of this study was to evaluate the concordance between these two methods and identify potential limitations of NGS implementation.

Methods

Thirty cases with MET amplification detected by FISH were retrospectively selected from a cohort of 567 LUAD diagnosed between 2018 and 2022 (prevalence: 5.3%). Cases were classified according to the current Camidge-2021 FISH criteria as 5 low-amplified (MET/CEP7 ratio ≥1.8 to ≤2.2), 11 medium-amplified (MET/CEP7 ratio >2.2 to <4) and 14 high-amplified (MET/CEP7 ratio ≥4). Tumor area and tumor cell percentage were annotated to later evaluate complete molecular alterations by NGS using the Oncomine Precision Assay.

Results

Detection of MET amplification was concordant in only 16 out of 30 cases (5 cases were excluded due to insufficient DNA), and no correlation was found between MET copy number determined by FISH and NGS (R²=0.346). Distribution of amplification categories was random: 2 cases showed low-amplification, 7 medium-amplification, and 7 high-amplification. Slight differences were observed between concordant and discordant cases in: MET enumeration (12.4 vs. 9.3 gene copies), MET/CEP7 ratio (4.8 vs. 3.2), tumor area (15 vs. 11mm2), and DNA concentration (12 vs. 7 ng/μl), but none of them were statistically significant. FISH results of the 9 discordant cases were reviewed and high copy number heterogeneity was observed in 7 of them and focal amplifications were observed in 2. In 7 out of 9 discordant cases, co-alterations were detected: 2 KRAS (p.G12C and p.Q61H), 2 BRAF non-V600, 2 MET exon 14 skipping and one EGFR p.L858R.

Conclusions

The detection of MET amplification by NGS did not show satisfactory concordance with the results obtained by FISH, likely due to the high heterogeneity in MET gene copy number enumeration. As a result, complementary determination by FISH is necessary, given the lack of standardized criteria for establishing CNAs positivity by NGS.

Clinical trial identification

Editorial acknowledgement

Legal entity responsible for the study

The authors.

Funding

Has not received any funding.

Disclosure

All authors have declared no conflicts of interest.